Rett syndrome is a developmental disorder that restricts brain growth beginning in the first year of life and evidence from neuropathology and neuroimaging indicates that axonodendritic connections are especially vulnerable. In a study of amino acid neurotransmitter receptors using receptor autoradiography in tissue slices of frontal cortex and the basal ganglia, we found a biphasic age-related pattern with relatively high receptor densities in young RS girls and lower densities at later time. Using microarray analysis of gene expression in frontal cortex, we found that some of the most prominent alterations occurred in gene products related to synapses, including the NMDA receptor NR1 subunit, the cytoskeletal protein MAP-2 and synaptic vesicle proteins. Using a new antibody that recognizes MeCP2, the transcription factor mutated in RS, we established that most neurons in the rodent brain express this transcription factor. We hypothesize that a major effect of mutations in the MeCP2 protein is to cause age-related disruption of synaptic proliferation and pruning in the first decade of life.